A comparative analysis of microbial DNA preparation methods for use with massive and branching coral growth forms

Hernandez-Agreda, Alejandra, Leggat, William, and Ainsworth, Tracy D. (2018) A comparative analysis of microbial DNA preparation methods for use with massive and branching coral growth forms. Frontiers In Microbiology, 9. 2146.

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View at Publisher Website: https://doi.org/10.3389/fmicb.2018.02146
 
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Abstract

In the last two decades, over 100 studies have investigated the structure of the coral microbiome. However, as yet there are no standardized methods applied to sample preservation and preparation, with different studies using distinct methods. There have also been several comparisons made of microbiome data generated across different studies, which have not addressed the influence of the methodology employed over each of the microbiome datasets. Here, we assess three different preservation methods; salt saturated dimethyl sulfoxide (DMSO) - EDTA, snap freezing with liquid nitrogen and 4% paraformaldehyde solution, and two different preparation methodologies; bead beating and crushing, that have been applied to study the coral microbiome. We compare the resultant bacterial assemblage data for two coral growth forms, the massive coral Goniastrea edwardsi and the branching coral Isopora palifera. We show that microbiome datasets generated from differing preservation and processing protocols are comparable in composition (presence/absence). Significant discrepancies between preservation and homogenization methods are observed in structure (relative abundance), and in the occurrence and dominance of taxa, with rare (low abundance and low occurrence) phylotypes being the most variable fraction of the microbial community. Finally, we provide evidence to support chemical preservation with DMSO as effective as snap freezing samples for generating reliable and robust microbiome datasets. In conclusion, we recommend where possible a standardized preservation and extraction method be taken up by the field to provide the best possible practices for detailed assessments of symbiotic and conserved bacterial associations.

Item ID: 55703
Item Type: Article (Research - C1)
ISSN: 1664-302X
Keywords: coral microbiome, bacteria, microbial ecology, DESS, paraformaldehyde, snap frozen, bead beating, crushing
Copyright Information: Copyright © 2018 Hernandez-Agreda, Leggat and Ainsworth. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Funders: Australian Research Council Centre of Excellence for Coral Reef Studies (ARC CoE Coral Reef Studies), Australian Research Council (ARC), James Cook University (JCU), AusAID
Projects and Grants: JCU Higher Degree Research Enhancement Scheme, ARC Discovery Program scheme
Date Deposited: 26 Sep 2018 08:11
FoR Codes: 06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060503 Microbial Genetics @ 100%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 100%
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